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POCython: "fatal error: numpy/arrayobject.h: No such file or directory"
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copied!<p>I'm trying to speed up the answer <a href="https://stackoverflow.com/a/14469557/1658908">here</a> using Cython. I try to compile the code (after doing the <code>cygwinccompiler.py</code> hack explained <a href="https://stackoverflow.com/questions/6034390/compiling-with-cython-and-mingw-produces-gcc-error-unrecognized-command-line-o/6035864#6035864">here</a>), but get a <code>fatal error: numpy/arrayobject.h: No such file or directory...compilation terminated</code> error. Can anyone tell me if it's a problem with my code, or some esoteric subtlety with Cython?</p> <p>Below is my code. Thanks in advance:</p> <pre><code>import numpy as np import scipy as sp cimport numpy as np cimport cython cdef inline np.ndarray[np.int, ndim=1] fbincount(np.ndarray[np.int_t, ndim=1] x): cdef int m = np.amax(x)+1 cdef int n = x.size cdef unsigned int i cdef np.ndarray[np.int_t, ndim=1] c = np.zeros(m, dtype=np.int) for i in xrange(n): c[<unsigned int>x[i]] += 1 return c cdef packed struct Point: np.float64_t f0, f1 @cython.boundscheck(False) def sparsemaker(np.ndarray[np.float_t, ndim=2] X not None, np.ndarray[np.float_t, ndim=2] Y not None, np.ndarray[np.float_t, ndim=2] Z not None): cdef np.ndarray[np.float64_t, ndim=1] counts, factor cdef np.ndarray[np.int_t, ndim=1] row, col, repeats cdef np.ndarray[Point] indices cdef int x_, y_ _, row = np.unique(X, return_inverse=True); x_ = _.size _, col = np.unique(Y, return_inverse=True); y_ = _.size indices = np.rec.fromarrays([row,col]) _, repeats = np.unique(indices, return_inverse=True) counts = 1. / fbincount(repeats) Z.flat *= counts.take(repeats) return sp.sparse.csr_matrix((Z.flat,(row,col)), shape=(x_, y_)).toarray() </code></pre>

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